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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('wavClusteR_2.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing wavClusteR ───────────────────────────────────────────────────────
✔ Package installed successfully
── wavClusteR session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNWpU3K/file1534f763811149/wavClusteR
→ BiocVersion: 3.24
→ Package: wavClusteR
→ PackageVersion: 2.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/wavClusteR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNWpU3K/file1534f763811149/wavClusteR
→ installDir: /tmp/RtmpNWpU3K/file1534f73cf371a4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on wavClusteR ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.2 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: ATACSeq,
Coverage, MotifAnnotation, MotifDiscovery, Alignment,
MultipleSequenceAlignment, QualityControl, DataImport
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (56%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of wavClusteR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/getClusters.R (line 218, column 32)
    • require() in R/processMD.R (line 16, column 32)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getAllSub.R (line 101, column 19)
    • R/plotSubstitutions.R (line 74, column 31)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • annotateClusters.R (line 199, column 35)
    • ...
    • getMeta.R (line 442, column 28)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/annotateClusters.R (line 224, column 17)
    • print() in R/plotSizeDistribution.R (line 72, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getClusters.R (line 223, column 13)
    • ...
    • R/processMD.R (line 26, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/getClusters.R (line 218, column 14)
  • ...
  • suppressWarnings() in R/processMD.R (line 16, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • estimateFDR() (R/FDRbyRSF.R): 175 lines
    • ...
    • filterClustersMRN() (R/filterClusters.R): 119 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • estimateFDR.Rd
    • ...
    • exportSequences.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 24% of man
pages use at least one of these tags.
  Found in files:
    • annotateClusters.Rd
    • ...
    • getMetaTSS.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • annotateClusters.Rd
    • ...
    • getMetaTSS.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 273 lines (8%) are > 80 characters long.
  First few lines:
    • R/annotateClusters.R#L46 #' Comoglio F, Sievers C and Paro R (201 ...
    • ...
    • vignettes/wavCluster_vignette.Rmd#L361 Sievers, C., Schlumpf, T.,
    Sawarkar, R., ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1414 lines (40%) contain tabs.
  First few lines:
    • R/annotateClusters.R#L63 #' cores = 1, ...
    • ...
    • vignettes/wavCluster_vignette.Rmd#L187 ``` ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 155 lines (4%) are
not.
  First few lines:
    • R/annotateClusters.R#L86 for a list of supp ...
    • ...
    • vignettes/wavCluster_vignette.Rmd#L308 verbose = TRUE ) ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the wavClusteR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.